integrated new routine

"book_content.md" was moved to "LoC.md" (list of contents) and edited; "construct_toc.py" was integrated into "update.py", a copy is kept at "update_ToC.py". From now on, new proofs and definitions should be entered into "LoC.md", not "ToC.md"

Author: JoramSoch

book_content.md I/LoC.mdbook_content.md renamed to I/LoC.md

@@ -1,3 +1,12 @@
+---
+layout: page
+title: "List of Contents"
+---
+
+
+Templates: **[Proof](/P/-temp-)** – *[Definition](/D/-temp-)*
+
+
 # Chapter I: General Theorems
 ## Probability theory
 ### Random experiments

I/ToC.md

@@ -12,7 +12,7 @@ title: "Table of Contents"
 <br>
 <h3 id="General Theorems">Chapter I: General Theorems</h3>
 
-   
+
 1. <p id="Probability theory">Probability theory</p>
 
    <p id="Random experiments"></p>
@@ -250,7 +250,7 @@ title: "Table of Contents"
    &emsp;&ensp; 1.21.7. **[First central moment is zero](/P/momcent-1st)** <br>
    &emsp;&ensp; 1.21.8. **[Second central moment is variance](/P/momcent-2nd)** <br>
    &emsp;&ensp; 1.21.9. *[Standardized moment](/D/mom-stand)* <br>
-   
+
 2. <p id="Information theory">Information theory</p>
 
    <p id="Shannon entropy"></p>
@@ -303,7 +303,7 @@ title: "Table of Contents"
    &emsp;&ensp; 2.5.8. **[Invariance under parameter transformation](/P/kl-inv)** <br>
    &emsp;&ensp; 2.5.9. **[Relation to discrete entropy](/P/kl-ent)** <br>
    &emsp;&ensp; 2.5.10. **[Relation to differential entropy](/P/kl-dent)** <br>
-   
+
 3. <p id="Estimation theory">Estimation theory</p>
 
    <p id="Basic concepts of estimation"></p>
@@ -320,7 +320,7 @@ title: "Table of Contents"
    3.3. Interval estimates <br>
    &emsp;&ensp; 3.3.1. *[Confidence interval](/D/ci)* <br>
    &emsp;&ensp; 3.3.2. **[Construction of confidence intervals using Wilks' theorem](/P/ci-wilks)** <br>
-   
+
 4. <p id="Frequentist statistics">Frequentist statistics</p>
 
    <p id="Likelihood theory"></p>
@@ -356,7 +356,7 @@ title: "Table of Contents"
    &emsp;&ensp; 4.3.11. **[Distribution of p-value under null hypothesis](/P/pval-h0)** <br>
    &emsp;&ensp; 4.3.12. *[Minimum detectable effect](/D/mde)* <br>
    &emsp;&ensp; 4.3.13. *[Minimum required sample size](/D/mrss)* <br>
-   
+
 5. <p id="Bayesian statistics">Bayesian statistics</p>
 
    <p id="Probabilistic modeling"></p>
@@ -398,7 +398,7 @@ title: "Table of Contents"
    &emsp;&ensp; 5.3.5. *[Variational Bayes](/D/vb)* <br>
    &emsp;&ensp; 5.3.6. **[Decomposition of the free energy](/P/fren-dec)** <br>
    &emsp;&ensp; 5.3.7. **[Free energy is lower bound on log model evidence](/P/fren-lme)** <br>
-   
+
 6. <p id="Machine learning">Machine learning</p>
 
    <p id="Scoring rules"></p>
@@ -415,7 +415,7 @@ title: "Table of Contents"
 <br>
 <h3 id="Probability Distributions">Chapter II: Probability Distributions</h3>
 
-   
+
 1. <p id="Univariate discrete distributions">Univariate discrete distributions</p>
 
    <p id="Discrete uniform distribution"></p>
@@ -467,7 +467,7 @@ title: "Table of Contents"
    &emsp;&ensp; 1.5.3. **[Mean](/P/poiss-mean)** <br>
    &emsp;&ensp; 1.5.4. **[Variance](/P/poiss-var)** <br>
    &emsp;&ensp; 1.5.5. **[Shannon entropy](/P/poiss-ent)** <br>
-   
+
 2. <p id="Multivariate discrete distributions">Multivariate discrete distributions</p>
 
    <p id="Categorical distribution"></p>
@@ -487,7 +487,7 @@ title: "Table of Contents"
    &emsp;&ensp; 2.2.5. **[Covariance](/P/mult-cov)** <br>
    &emsp;&ensp; 2.2.6. **[Shannon entropy](/P/mult-ent)** <br>
    &emsp;&ensp; 2.2.7. **[Marginal distributions](/P/mult-marg)** <br>
-   
+
 3. <p id="Univariate continuous distributions">Univariate continuous distributions</p>
 
    <p id="Continuous uniform distribution"></p>
@@ -637,7 +637,7 @@ title: "Table of Contents"
    &emsp;&ensp; 3.11.5. **[Variance](/P/exg-var)** <br>
    &emsp;&ensp; 3.11.6. **[Skewness](/P/exg-skew)** <br>
    &emsp;&ensp; 3.11.7. **[Method of moments](/P/exg-mome)** <br>
-   
+
 4. <p id="Multivariate continuous distributions">Multivariate continuous distributions</p>
 
    <p id="Multivariate normal distribution"></p>
@@ -696,7 +696,7 @@ title: "Table of Contents"
    &emsp;&ensp; 4.5.2. **[Probability density function](/P/dir-pdf)** <br>
    &emsp;&ensp; 4.5.3. **[Kullback-Leibler divergence](/P/dir-kl)** <br>
    &emsp;&ensp; 4.5.4. **[Exceedance probabilities](/P/dir-ep)** <br>
-   
+
 5. <p id="Matrix-variate continuous distributions">Matrix-variate continuous distributions</p>
 
    <p id="Matrix-normal distribution"></p>
@@ -730,7 +730,7 @@ title: "Table of Contents"
 <br>
 <h3 id="Statistical Models">Chapter III: Statistical Models</h3>
 
-   
+
 1. <p id="Univariate normal data">Univariate normal data</p>
 
    <p id="Univariate Gaussian"></p>
@@ -873,7 +873,7 @@ title: "Table of Contents"
    &emsp;&ensp; 1.7.2. **[Posterior distribution](/P/blrkc-post)** <br>
    &emsp;&ensp; 1.7.3. **[Log model evidence](/P/blrkc-lme)** <br>
    &emsp;&ensp; 1.7.4. **[Accuracy and complexity](/P/blrkc-anc)** <br>
-   
+
 2. <p id="Multivariate normal data">Multivariate normal data</p>
 
    <p id="Multivariate Gaussian"></p>
@@ -915,7 +915,7 @@ title: "Table of Contents"
    &emsp;&ensp; 2.5.1. **[Conjugate prior distribution](/P/mblr-prior)** <br>
    &emsp;&ensp; 2.5.2. **[Posterior distribution](/P/mblr-post)** <br>
    &emsp;&ensp; 2.5.3. **[Log model evidence](/P/mblr-lme)** <br>
-   
+
 3. <p id="Count data">Count data</p>
 
    <p id="Binomial observations"></p>
@@ -961,7 +961,7 @@ title: "Table of Contents"
    &emsp;&ensp; 3.4.3. **[Conjugate prior distribution](/P/poissexp-prior)** <br>
    &emsp;&ensp; 3.4.4. **[Posterior distribution](/P/poissexp-post)** <br>
    &emsp;&ensp; 3.4.5. **[Log model evidence](/P/poissexp-lme)** <br>
-   
+
 4. <p id="Frequency data">Frequency data</p>
 
    <p id="Beta-distributed data"></p>
@@ -978,7 +978,7 @@ title: "Table of Contents"
    4.3. Beta-binomial data <br>
    &emsp;&ensp; 4.3.1. *[Definition](/D/betabin-data)* <br>
    &emsp;&ensp; 4.3.2. **[Method of moments](/P/betabin-mome)** <br>
-   
+
 5. <p id="Categorical data">Categorical data</p>
 
    <p id="Logistic regression"></p>
@@ -991,7 +991,7 @@ title: "Table of Contents"
 <br>
 <h3 id="Model Selection">Chapter IV: Model Selection</h3>
 
-   
+
 1. <p id="Goodness-of-fit measures">Goodness-of-fit measures</p>
 
    <p id="Residual variance"></p>
@@ -1024,7 +1024,7 @@ title: "Table of Contents"
    &emsp;&ensp; 1.4.1. *[Definition](/D/snr)* <br>
    &emsp;&ensp; 1.4.2. **[Relationship to coefficient of determination](/P/snr-rsq)** <br>
    &emsp;&ensp; 1.4.3. **[Relationship to maximum log-likelihood](/P/snr-mll)** <br>
-   
+
 2. <p id="Classical information criteria">Classical information criteria</p>
 
    <p id="Akaike information criterion"></p>
@@ -1043,7 +1043,7 @@ title: "Table of Contents"
    2.3. Deviance information criterion <br>
    &emsp;&ensp; 2.3.1. *[Definition](/D/dic)* <br>
    &emsp;&ensp; 2.3.2. *[Deviance](/D/dev)* <br>
-   
+
 3. <p id="Bayesian model selection">Bayesian model selection</p>
 
    <p id="Model evidence"></p>

update.py

@@ -17,7 +17,7 @@
 E-Mail: joram.soch@bccn-berlin.de
 
 First edit: 2019-09-27 12:55:00
- Last edit: 2025-10-31 15:35:00
+ Last edit: 2025-12-12 16:06:00
 """
 
 
@@ -141,36 +141,97 @@
 print('   - ' + str(num_def) + ' files found in definition directory!')
 
 
-# Table of Contents: read index file
+# List of Contents: read index file
 #-----------------------------------------------------------------------------#
-print('\n1. Table of Contents:')
-f1   = open('I/ToC.md', 'r')
-ToCs = f1.readlines()
-f1.close()
+print('\n1a.List of Contents:')
+f1a  = open('I/LoC.md', 'r')
+LoCs = f1a.readlines()
+f1a.close()
 
-# Table of Contents: check for proof Shortcuts
+# List of Contents: check for proof shortcuts
 #-----------------------------------------------------------------------------#
 incl = np.zeros(num_pr, dtype=bool)
 for (i, proof) in enumerate(proofs):
-    for line in ToCs:
+    for line in LoCs:
         if line.find('(/P/' + proof['shortcut'] + ')') > -1:
             incl[i] = True
     if ~incl[i]:
-        print('   - WARNING: proof "' + proof['shortcut'] + '" is not in table of contents!')
-if all(incl):
-    print('   - ' + str(sum(incl)) + ' proofs found in table of contents!')
+        print('   - WARNING: proof "' + proof['shortcut'] + '" is not in list of contents!')
+print('   - ' + str(sum(incl)) + ' proofs found in list of contents!')
 
-# Table of Contents: check for definition Shortcuts
+# List of Contents: check for definition shortcuts
 #-----------------------------------------------------------------------------#
 incl = np.zeros(num_def, dtype=bool)
 for (i, definition) in enumerate(defs):
-    for line in ToCs:
+    for line in LoCs:
         if line.find('(/D/' + definition['shortcut'] + ')') > -1:
             incl[i] = True
     if ~incl[i]:
-        print('   - WARNING: definition "' + definition['shortcut'] + '" is not in table of contents!')
-if all(incl):
-    print('   - ' + str(sum(incl)) + ' definitions found in table of contents!')
+        print('   - WARNING: definition "' + definition['shortcut'] + '" is not in list of contents!')
+print('   - ' + str(sum(incl)) + ' definitions found in list of contents!')
+
+
+# Table of Contents: prepare index file
+#-----------------------------------------------------------------------------#
+print('\n1b.Table of Contents:')
+print('   - generating from list of contents ...')
+f1b = open('I/ToC.md', 'w')
+f1b.write('---\nlayout: page\ntitle: "Table of Contents"\n---\n\n\n')
+f1b.write('**[Proofs](/P/-temp-)** are printed in **bold** – *[Definitions](/D/-temp-)* are set in *italics* <br>\n')
+f1b.write('**Proofs**: [by Number](/I/PbN), [by Topic](/I/PbT) – *Definitions*:  [by Number](/I/DbN), [by Topic](/I/DbT) <br>\n')
+f1b.write('<u>Specials:</u> [General Theorems](/S/ChI), [Probability Distributions](/S/ChII), [Statistical Models](/S/ChIII), [Model Selection Criteria](/S/ChIV) <br>\n')
+
+# Table of Contents: write all chapters
+#-----------------------------------------------------------------------------#
+roman    = ['I', 'II', 'III', 'IV', 'V']
+num_chap = 0
+num_sect = 0
+num_ssec = 0
+num_item = 0
+
+# check list of contents
+for line in LoCs:
+    line = line.strip()
+    
+    # this is a new chapter
+    if line.startswith("# Chapter "):
+        num_sect  = 0
+        num_chap  = num_chap + 1
+        curr_chap = line[line.find(': ')+2:].strip()
+        f1b.write('\n\n<br>\n')
+        f1b.write('<h3 id="{}">Chapter {}: {}</h3>\n\n'. \
+                  format(curr_chap, roman[num_chap-1], curr_chap))
+    
+    # this is a new section
+    elif line.startswith('## '):
+        num_ssec  = 0
+        num_sect  = num_sect + 1
+        curr_sect = line[line.find('## ')+3:].strip()
+        f1b.write('\n')
+        f1b.write('{}. <p id="{}">{}</p>\n'. \
+                  format(num_sect, curr_sect, curr_sect))
+    
+    # this is a new subsection
+    elif line.startswith('### '):
+        num_item  = 0
+        num_ssec  = num_ssec + 1
+        curr_ssec = line[line.find('### ')+4:].strip()
+        f1b.write('   \n')
+        f1b.write('   <p id="{}"></p>\n'.format(curr_ssec))
+        f1b.write('   {}.{}. {} <br>\n'. \
+                  format(num_sect, num_ssec, curr_ssec))
+    
+    # this is a new item
+    elif line.startswith('- '):
+        num_item  = num_item + 1
+        curr_item = line[line.find('- ')+2:].strip()
+        f1b.write('   &emsp;&ensp; {}.{}.{}. {} <br>\n'. \
+                  format(num_sect, num_ssec, num_item, curr_item))
+
+f1b.close()
+del num_chap,  num_sect,  num_ssec,  num_item
+del curr_chap, curr_sect, curr_ssec, curr_item
+print('     successfully written to disk!')
 
 
 # Proof by Number: prepare index file